Abstract: In order to understand the basic features of the whole chloroplast genome of Clivia and to develop molecular markers for germplasm utilization analysis. Six Clivia species were chosen for research, with finely spliced and efficiently assembled of their chloroplast genomes, along with comprehensive gene annotation. The results were as follows: The chloroplast genome lengths of C. gardenii, C. miniata var. citrina, C. miniata var. Variegata, C. robusta, C. caulescens and C. miniata were 158 156, 158 112, 157 689, 157 130, 157 130, 158 149, and 158 114 bp, respectively. 130, 130, 133, 128, 128, and 133 genes were annotated, respectively. 54, 60, 61, 63, 71, and 61 SSRs were identified in the chloroplast genomes of C. gardenii, C. miniata var.citrina, C. miniata var. variegata, C. robusta, C. caulescens and C. miniata, respectively. Among the coding regions, the ycf4-cemA gene had the highest nucleotide diversity value(P_i=0.0152), as well as the rrn23 gene, which had a nucleotide diversity value greater than 0.0100 and can be considered as genes with higher diversity. The Rpl22 gene is located at the junction between the LSC(Large Single Copy region) and IRb(Inverted Repeat region b), with a difference of only 1 bp among 6 species. Specifically, the ndhF gene spans the border region between the IRb and the SSC and is only 6 bp different in sequence among these species. Among them, C. gardenii, C. robusta, C. caulescens are the same, while the other three species of C. miniata, C. miniata var. citrina, and C. miniata var. variegata are the same. Two highly differentiated genes(rpoC2 and ycf2) and 8 highly variable regions(rps19-psbA, rps16-trnS-GCU, atpF-atpH, trnT-UGU-trnF-GAA, rps2-rpoC2, petA-psbL, trnI-CAU-ycf2, rps12-rrn16). Comparative analysis of the monarch chloroplast genome allows for the utilization of highly divergent genes and highly variable regions in order to develop highly specific molecular markers.